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Our lab investigates the causes and consequences of fungal community formation, including the roles of fungi in symbioses and landscape-scale biogeochemical dynamics.

We have projects investigating a broad suite of topics in fungal ecology, including:

Lifestyle influences on the human oral mycobiome

Undergrads Harrison Haws and Nicholas Long are leading this project. They are interested in the fungi that live in human mouths and whether diet and/or exercise have an effect on the core communities present. We have sampled oral rinses from 188 individuals and are amplifying the ITS1 region of ribosomal-encoding DNA for sequencing to compare the community structure of fungi between groups of people.

Fungal community recovery from forest fires

Undergrads Alyssa Tidwell and Spencer McGee are leading this project. Soil fungi from paired burned/un-burned sites in the Wasatch and Uinta Mountains are being sequenced and cultured. Our sampling includes fire sites from ~20 years ago to recently burned areas. We are interested in the time it takes for forest soil fungal communities to recover after a burn and whether the character of the recovered community influences plant recovery. This project is being carried out in collaboration with the Utah Department of Natural Resources – Division of Forestry, Fire, and State Lands.

Salinity constraints on aquatic fungi in The Great Salt Lake

Image credit: Deseret.com

Undergrads McRae Bingelli, Joseph Jimenez, Kyle Palmer, and Alyssa Tidwell are leading this project. We are curious about the fungi that inhabit the hypersaline environment of the Great Salt Lake, and are sampling water and sediment along a salinity gradient from a freshwater input source up through the extremely hypersaline northern half of the lake. This project is in collaboration with the Utah Department of Natural Resources – Division of Forestry, Fire, and State Lands. It aims to collect baseline data on the microbial food web in this important habitat and explore the environmental limits of extremophilic fungi.

Endophytes in critically-endangered cacti

Image credit: Wiki commons

Undergrad Tyler Hacking is leading this project. Working with Capitol Reef National Park, we are developing a non-detrimental method to track endophitic fungi in critically-endangered cacti. Once validated, this method will then be used to explore the role of fungal symbionts in alleviating pathogen damage and herbivory for these endemic cacti.

Habitat connectivity and selection in Hawaiian fungi

We have previously found that some fungi turn up in wildly different habitats (e.g., inside the leaves of plants at the top of a mountain and in deep mesophotic coral reefs). With the help of several teams, we have put together a massive amplicon data set of environmental fungi from all over the Hawaiian islands, including soil, water, plant, insect gut, and air samples. We are using these data to investigate habitat connectivity and the relative importance of dispersal vs. niche selection.

The Mauna Loa Observatory is most famous as the location where the CO2 data for the Keeling Curve were generated. It has been continuously observing atmospheric processes since the 1950s. We are using a 12-year long archive of air filters from this site to investigate the long-term trends in fungal dispersal in the upper atmosphere. These filters have been sucking up some of the cleanest air on the planet to observe fine particulate matter in the atmosphere and, in the process, trapping fungal spores. Carefully preserved, they represent something like a fossil record of transcontinental fungal dispersal. By sequencing the genetic material trapped in the filters we are able to link long-distance fungal dispersal to climate patterns.

(The following are less-current projects I am wrapping up)

We are looking at the factors that shape the establishment of fungal communities in the phyllosphere (on and in plant leaves). All plants are closely associated with fungi, and these commensal microbes may provide strong benefits to the plants by fending off potential pathogens, for example. We are interested in better understanding how the genetic relatedness of fungal species influences the outcome of fungal leaf-colonization events. This may be particularly important in a place like Hawaii where human-introduced microbial pathogens may pose substantial threats to rare and endemic plant species. We are testing the theoretical aspect of this work in the model host, Arabidopsis thalliana and testing a practical application in the critically endangered Hawaiian mint, Phyllostegia kaalaensis, by experimentally transplanting endophyte communities from healthy wild individuals into previously-sterile individuals in a greenhouse which are highly susceptible to foliar pathogens and tracking the establishment of the fungal community along with plant responses to stress. The use of A. thalliana, in conjunction, will allow us to potentially examine the role that the host plant genome plays in the establishment of these fungal communities. This photo shows one of the last remaining wild individuals of P. mollis on earth. Perhaps the endophyte community associated with these healthy wild individuals can be used to improve outplanting success in the “captive” population. See the paper here: https://peerj.com/articles/4020/

Phyllosphere fungi in the diet of the endangered Oahu Tree Snail (Gallery)

The adorable tree snail Achatinella mustelina is found only in a few locations on the island of Oahu. It has a fascinating life history that includes giving birth to live young, but it is poorly adapted for the recent influx of competitors and predators into its habitat. Recent programs through the Army Environmental Division have shown some success, but depend on relocating wild populations of these snails to predator-free exclosures… a process that involves some risk to the snails. I am working with the Army to determine whether transplanting the epiphytic fungi that the snails use as food will benefit their establishment in their new locations. With such a slow dispersal rate historically, there are several genetically distinct populations on the island and the hope is to do everything possible to ease their transition into their new safe havens.

Soils cover most of the Earth’s terrestrial surface and have an indispensable function in the global cycling of carbon, nitrogen, phosphorous and sulfur. A key component of soils is the assemblage of organisms present, members of which are responsible for carrying out many small scale processes that underlie environmentally important functions. The immense complexity of soil communities and extreme difficulty of obtaining unequivocal data from field studies has led many researchers to treat soil ecosystem processes as a “black box” with little attention paid to community or organism level response. More recently, greater efforts have been made to escape from this black box approach and mechanistically investigate microbe-mediated processes in relation to the members present in the community. Working to understand the interactions of these individuals will help to shine a light into the black box of soil systems and illuminate some of the fundamental processes occurring there.
One of the most important processes occurring in soils is the carbon (C) cycle. Soil organic C is the largest reservoir of C in the so-called “fast C cycle” on earth and soils are the ultimate destination of the vast majority of photosynthetically-fixed C in terrestrial ecosystems. Eventually, this fixed C (organic matter) is decomposed by soil biota (mainly bacteria and fungi) and returned to the atmosphere as CO2 (a greenhouse gas) but decomposition rates are controlled by a variety of factors including microbial activity and climate. As global climate change has become a pressing reality, there has been much concern over the fate of soil C under warming conditions. It has been well established that any increase in temperature leads to exponentially greater rates of CO2 losses from soil to the atmosphere and there is much debate over whether soils may enter a positive feedback loop and become a net source of greenhouse gasses globally leading to strengthened global warming scenarios. A comparison among global C cycle models revealed a severe discrepancy in terms of future warming effects on soil C decomposition rates, suggesting a strong need to better understand the decomposition process and its temperature sensitivity.
Despite active research in the past two decades the factors controlling temperature sensitivity of soil C decomposition (often expressed as Q10 – proportional increase in CO2 released by soil heterotrophic microbes for a 10oC increase in temperature) remain poorly understood. While soil C quality, soil temperature/moisture, and carbon input rates have been shown to affect Q10, how soil fauna and their predation on bacteria and fungi affects overall soil C decomposition Q10 is virtually unstudied. Specifically, while the direct roles of certain bacterial and fungal groups have been given considerable attention, far fewer studies have addressed the influence of protists within these models.

My project utilizes manipulated soil microcosms and high-throughput DNA sequencing to tease apart the roles that amoeboid predators have in shaping bacterial communities and how this role is influenced by a changing climate.

Biogeography of amoebae

The ongoing debate over the global distribution of microbes features two main paradigms: “everything is everywhere” (EiE), referring to cosmopolitan distributions of microbes selected only by local environmental variables and “moderate endemism” (ME), with the contrasting claim that many microbial species display patchy distributions even within suitable environments. Much effort has been devoted to testing these models and it seems clear that some protist species do appear to have limited geographic ranges though it remains unclear as to which factors (species age, availability of dispersal vectors, adaptations for dispersal, or availability of local habitats) are lacking in suitability to facilitate EiE distributions for these species. The use of “flagship” species that exhibit “conspicuous size, morphology, and/or colour” has been proposed as an effective way to test the EiE model in specific cases such as testate amoebae, but little attention has been given to distributions of naked amoebae, largely due to the difficulty associated with their accurate identification.

Protosteloid amoebae, formerly known as protostelids, are a paraphyletic assemblage of naked amoebae scattered widely across the Amoebozoa supergroup and are characterized by a shared ability to form distinctive fruiting bodies consisting of one or a few spores on an acellular stalk. They fit the qualifications of a “flagship” group since the fruiting bodies are conspicuous (from 10 to >100 µm) and morphologically distinctive, and have varied microhabitat requirements. Additionally, nearly one third of the 28 described morphospecies exhibit ballistosporous dispersal and the most common species, Protostelium mycophaga, is known to readily and successfully disperse via airborne spores.

My project utilized a massive dataset of culture-based observations of protosteloid amoebae from around the globe to look for patterns in or potential barriers to their distributions.